Publications

Peer-Reviewed Papers and Book Chapters

Publications from Tamamis lab

• Jonnalagadda SVR, Ornithopoulou E, Orr AA, Mossou E, Forsyth E, Mitchell EP, Bowler MW, Mitraki A Tamamis P. Computational Design of Amyloid Self-Assembling Peptides Bearing Aromatic Residues and the Cell Adhesive Motif Arg-Gly-Asp. Mol. Syst. Des. Eng. 2017, Mol. Syst. Des. Eng., 2017. 2:321-335.

• Deidda G, Spies JW, Ranella A, Mossou E, Forsyth VT, Mitchell EP, Bowler MW, Tamamis P, Mitraki A. Self-assembled amyloid peptides with Arg-Gly-Asp (RGD) motifs as scaffolds for tissue engineering. ACS Biomater. Sci. Eng., 2017, 3 (7):1404–1416.

• Khoury GA, Smadbeck J, Kieslich CA, Koskosidis AJ, Guzman YA, Tamamis P, Floudas CA. Princeton_TIGRESS 2.0: High refinement consistency and net gains through support vector machines and molecular dynamics in double-blind predictions during the CASP11 experiment. Proteins. 2017, 85(6):1078-1098.

• Orr A, Wördehoff MM, Hoyer W, Tamamis P. Uncovering the Binding and Specificity of β-Wrapins for Amyloid-β and α-Synuclein. J. Phys. Chem. B 2016, 120 (50): 12781–12794.

• Cheng Y, Jin UH, Davidson LA, Chapkin RS, Jayaraman A, Tamamis P, Orr A, Allred C, Denison MS, Soshilov A, Weaver E, Safe S. Microbial-Derived 1,4-Dihydroxy-2-naphthoic Acid and Related Compounds as Aryl Hydrocarbon Receptor Agonists/Antagonists: Structure-Activity Relationships and Receptor Modeling. Toxicological Sciences 2016, 155 (2): 458-473.

• Kieslich CA, Tamamis P, Guzman YA, Onel M, Floudas CA. Highly Accurate Structure-Based Prediction of HIV-1 Coreceptor Usage Suggests Intermolecular Interactions Driving Tropism. PLoS One. 2016, 11(2): e0148974.

Publications of Phanourios Tamamis from 2006-2015

	• Gorham RD Jr, Forest, DL, Khoury, GA, Beecher CN, Tamamis P, Archontis, G, Larive, CK, Floudas, C A, Radeke, M J, Johnson, LV, Morikis, D New compstatin peptides containing N-terminal extensions and non-natural amino acids exhibit potent complement inhibition and improved solubility characteristics. Journal of Medicinal Chemistry 2015, 58(2): 814-826.
	• Tamamis P, Floudas, CA. Elucidating a Key Anti-HIV-1 and Cancer-Associated Axis: The Structure of CCL5 (Rantes) in Complex with CCR5. Scientific Reports 2014, 4: 5447.
	• Tamamis P, Floudas, CA. Elucidating a Key Component of Cancer Metastasis: CXCL12 (SDF-1α) Binding to CXCR4. Journal of Chemical Information and Modeling 2014, 54 (4): 1174-1188.
	• Tamamis P, Floudas, CA. Molecular Recognition of CCR5 by an HIV-1 gp120 V3 Loop. PLoS ONE 2014, 9 (4): e95767.
	• Tamamis P, Terzaki, K, Kassinopoulos M, Mastrogiannis L, Mossou E, Forsyth VT, Mitchell EP, Mitraki A, Archontis G. Self-Assembly of an Aspartate-Rich Sequence from the Adenovirus Fibre Shaft: Insights from Molecular Dynamics Simulations and Experiments. Journal of Physical Chemistry B 2014, 118 (7): 1765-1774.
	• Khoury GA, Smadbeck J, Tamamis, P, Vandris AC, Kieslich CA, Floudas CA Forcefield_NCAA: Ab Initio Charge Parameters to Aid in the Discovery and Design of Therapeutic Proteins and Peptides with Unnatural Amino Acids and Their Application to Complement Inhibitors of the Compstatin Family. ACS Synthetic Biology, 2014, 3(12): 855–869.
	• Khoury GA, Tamamis P, Pinnaduwage N, Smadbeck J, Kieslich CA, Floudas CA. Princeton_TIGRESS: Protein geometry refinement using simulations and support vector machines. Proteins: Structure, Function, and Bioinformatics 2014, 82 (5): 794-814.
	• Tamamis P, Kasotakis, E, Archontis, G, Mitraki, A. Combination of Theoretical and Experimental Approaches for the Design and Study of Fibril-forming Peptides. In Protein Design: Methods and Applications. Methods Mol. Biol. 2014, 1216: 53-70.
	• Tamamis P, Kieslich, CA, Nikiforovich, GV, Woodruff, TM, Morikis, D, Archontis, G. Insights into the Mechanism of C5aR Inhibition by PMX53 via Implicit Solvent Molecular Dynamics Simulations and Docking. BMC Biophysics 2014, 7: 5.
	• Gorham RD Jr, Forest, DL, Tamamis P, López de Victoria A, Kraszni, M, Kieslich, CA, Banna, CD, Bellows-Peterson, ML, Larive, CK, Floudas, CA, Archontis, G, Johnson, LV, Morikis, D. Novel compstatin family peptides inhibit complement activation by drusen-like deposits in human retinal pigmented epithelial cell cultures. Experimental Eye Research2013, 116: 96-108.
	• Tamamis P, Floudas, CA. Molecular Recognition of CXCR4 by a Dual Tropic HIV-1 gp120 V3 Loop. Biophysical Journal 2013, 105 (6): 1502-1514.
	• Lopez de Victoria, A, Tamamis P, Kieslich, CA, Morikis, D. Insights into the Structure, Correlated Motions, and Electrostatic Properties of two HIV-1 gp120 V3 loops. PLoS ONE 2012, 7 (11): e49925.
	• Kieslich, CA, Tamamis P, Gorham RD Jr, Lopez de Victoria, A, Sausman, N, Archontis, G, Morikis, D. Exploring protein-protein and protein-ligand interactions in the immune system using molecular dynamics and continuum electrostatics. Current Physical Chemistry 2012, 2 (4): 324-343.
	• Tamamis P, Lopez de Victoria, A, Gorham, RD, Bellows-Peterson, ML, Pierou, P, Floudas, CA, Morikis, D, Archontis, G. Molecular Dynamics in Drug Design: New Generations of Compstatin Analogs. Chemical Biology & Drug Design 2012, 79 (5): 703-718.
	• Tamamis P, Pierou, P, Mytidou, C, Floudas, CA, Morikis, D, Archontis, G. Design of a modified mouse protein with ligand binding properties of its human analog by molecular dynamics simulations: The case of C3 inhibition by compstatin. Proteins: Structure, Function, and Bioinformatics 2011, 79 (11): 3166-3179.
	• Pieridou, G, Avgousti-Menelaou, C, Tamamis P, Archontis, G, Hayes, SC. UV Resonance Raman Study of TTR(105-115) Structural Evolution as a Function of Temperature. Journal of Physical Chemistry B 2011, 115 (14): 4088-4098.
	• Tamamis P, Archontis, G. Amyloid-like Self-Assembly of a Dodecapeptide Sequence from the Adenovirus Fiber Shaft: Perspectives from Molecular Dynamics Simulations. Journal of Non-Crystalline Solids 2011, 357 (2): 717-722.
	• Tamamis P, Morikis, D, Floudas, CA, Archontis, G. Species specificity of the complement inhibitor compstatin investigated by all-atom molecular dynamics simulations. Proteins 2010, 78 (12): 2655-2667.
	• Tamamis P, Kasotakis, E, Mitraki, A, Archontis, G. Amyloid-like Self-Assembly of Peptide Sequences from the Adenovirus Fiber Shaft: Insights from Molecular Dynamics Simulations. Journal of Physical Chemistry B 2009, 113 (47): 15639-15647.
	• Tamamis P, Adler-Abramovich, L, Reches, M, Marshall, K, Sikorski, P, Serpell, L, Gazit, E, Archontis, G. Self-Assembly of Phenylalanine Oligopeptides: Insights from Experiments and Simulations. Biophysical Journal 2009, 96 (12): 5020-5029.
	• Tamamis P, Skourtis, SS, Morikis, D, Lambris, JD, Archontis, G. Conformational analysis of Compstatin analogues with Molecular Dynamics Simulations in Explicit Water. Journal of Molecular Graphics and Modelling 2007, 26: 571-580.
	Conference Proceedings
	• Tamamis P, Lopez de Victoria, A, Gorham RD Jr, Bellows-Peterson, M, Floudas, CA, Morikis, D, Archontis, G. Insights into the Self- Iterative Computational and Experimental Drug Design Studies of the Complement Inhibitor Compstatin. IAS Series 2012, 8: 209-212.
	• Lopez de Victoria, A, Tamamis P, Gorham RD Jr, Bellows-Peterson, ML, Floudas, CA, Archontis, G, Morikis, D. Computational and Experimental Analysis of the Interactions Between C3 and Compstatin Family Peptides. Biophysical Journal 2012, 102, 3: 62a.
	• Gorham RD Jr, Lopez de Victoria, A, Tamamis P, Bellows, ML, Floudas, CA, Archontis, G, Morikis, D. Molecular dynamics simulations give insight into structure-activity relations and species specificity of compstatin – derived peptides. Abstracts of Papers of the American Chemical Society 2011, 241: 120-COMP.
	• Pieridou G, Avgousti-Menelaou, C, Tamamis P, Archontis, G, Hayes, SC. UV Resonance Raman Study of TTR(105-115) Structural Evolution as a Function of Temperature. AIP Conference Proceedings: XXII International Conference on Raman Spectroscopy 2010, 1267: 871-872.
	• Tamamis P, Adler-Abramovich, L, Gazit, E, Archontis, G. Insights into the Self-assembly of Phenylalanine Oligopeptides by Replica Exchange MD Simulations with the GBSW Implicit-Solvent Model. NIC Series (CBSB08 Proceedings) 2008, 40: 393-396.
	• Archontis G, Tamamis P, Skourtis, SS, Morikis D, Lambris, JD. Conformational analysis of Compstatin analogues with molecular dynamics simulations in explicit water. Molecular Immunology 2007, 44 (1): 150.
	• Tamamis P, Archontis G. Secondary structure of Compstatin analogues: Insights from molecular dynamics simulations in Explicit Water. NIC Series (CBSB06 Proceedings) 2006, 34: 133-136.